The variation of the surface mixed layer depth may affect not only the evolution of aquatic ecosystem, but also the temporal-spatial distribution of precipitation and climate in the basin. Based on the meteorological data and water temperature profiles observed in Erhai Lake (located in the Tibetan Plateau) and Taihu Lake (located in the Taihu Plain), the variation features and the mechanisms of the surface mixed layer depths are investigated. The stratification in Erhai Lake can be established and sustained in summer; the diurnal stratification in Erhai Lake can also be established, However, in both summer and autumn, stratification may exist in Taihu Lake. The time length of stratification is longer in Erhai Lake than that in Lake Taihu in the autumn. And the surface mixed layer depths in Erhai Lake are shallower than those in Taihu Lake in summer and autumn. The transformation frequency between establishment and destruction of stratification in Taihu Lake is faster than that in Erhai Lake, which illustrated that the response of water body in Taihu Lake to atmospheric variation is quicker than that in Erhai Lake. The water depth is a key factor which prevents such shallow lakes as Taihu Lake from establishing and maintainaning stratifications and in a suitable radiation condition the stratification will exist. The net radiation is a key factor that determines the stratification and the length of the time when the stratification can be sustained in lakes whose depths are the same as that of Erhai Lake. The research result in this paper is helpful for exploring the coupling mechanism of the turbulence of water and air and the evolution law of aquatic ecosystem.